Search Results
| Search type | Search syntax |
|---|---|
| Tags | [tag] |
| Exact | "words here" |
| Author |
user:1234 user:me (yours) |
| Score |
score:3 (3+) score:0 (none) |
| Answers |
answers:3 (3+) answers:0 (none) isaccepted:yes hasaccepted:no inquestion:1234 |
| Views | views:250 |
| Code | code:"if (foo != bar)" |
| Sections |
title:apples body:"apples oranges" |
| URL | url:"*.example.com" |
| Saves | in:saves |
| Status |
closed:yes duplicate:no migrated:no wiki:no |
| Types |
is:question is:answer |
| Exclude |
-[tag] -apples |
| For more details on advanced search visit our help page | |
Results tagged with protein-structure
Search options answers only
not deleted
user 10049
The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.
2
votes
How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?
Not sure but here https://biopython.org/docs/1.75/api/Bio.PDB.Residue.html Bio.PDB.Residue module Your can find :
add(self, atom) :
Add an Atom object.
Checks for adding duplicate atoms, and …
- 1,299
2
votes
Creating a PDB from a figure in paper
or you could taket it from :
https://www.rcsb.org/structure/7WMV pdb file
HETATM 4865 C13 1YI A 701 106.585 114.218 112.698 1.00 74.13 C
HETATM 4866 C15 1YI A 701 106.050 112.63 …
- 1,299
1
vote
How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?
OK my attempt, input pdb created in pymol with fab AVGLWPT , AVGLWPT , hydro=0 and saved as avgwpt.pdb :
ATOM 1 N ALA 1 67.846 51.727 15.161 1.00 0.00 N
ATOM 2 C …
- 1,299
2
votes
Accepted
How can I get a list of neighboring Hydrogen atoms of an alpha-carbon?
You posted similar question here: https://stackoverflow.com/questions/69676943/how-can-i-get-a-list-of-neighboring-hydrogen-atoms-of-an-alpha-carbon/69815509#69815509
ok got some code :
from Bio.PDB i …
- 1,299
1
vote
How can I measure the distance between each pair of carbon alphas in overlayed protein struc...
Ok, quite late.... my code stolen from https://pymolwiki.org/index.php/Spectrum as per in my comment:
Not an expert here, but you could try to create a pdb with only c-alpha where B factor column has …
- 1,299
2
votes
Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsio...
not able to grasp the question, tried to figure out a way to show the internal_coordinates:
from Bio.PDB import PDBParser, PICIO, PDBIO
# Read PDB entry.
parser = PDBParser(PERMISSIVE=1, QUIET=1)
st …
- 1,299
1
vote
Help me in understanding the PDB file
well wasnt able to figure out how to make openapigenerator work with rcsb pdb ModelServer https://models.rcsb.org/, I ended up with this code
copying the webserver manual input results for ligands:
im …
- 1,299
2
votes
How can I get the coordinates of Hydrogen atoms attached to alpha-carbon?
OK, tried to figure out a way using Biopython library, I believe there are tens of faster ways, having 1lkk_pdb_test.pdb as input :
ATOM 1 N LEU A 122 49.672 7.391 11.364 1.00 20.16 …
- 1,299
3
votes
What is the correct method of identifying the interacting residues for specific molecular do...
not an answer, just more inputs, but https://proteins.plus/5tl8#poseview
gives me this:
references:
ProteinsPlus: interactive analysis of protein–ligand binding interfaces
Molecular complexes at a g …
- 1,299
0
votes
BioPython internal_coords module returns different dihedral angles for the (seemingly) same ...
OK , visualizing both proteins in PyMOL , using set cartoon_gap_cutoff = 0 ,
I get :
Apparently the two conformations , have more than one difference in various loops.
I modify the code above , than …
- 1,299
5
votes
Accepted
Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordi...
ok, here my input pdb, example_short.pdb :
ATOM 1 N MET A 1 14.067 31.664 -1.639 1.00 80.87 N
ATOM 2 HN1 MET A 1 14.250 31.259 -0.699 1.00 0.00 …
- 1,299
1
vote
Accepted
Antibody self-aggregation: PDB structures
As per google search:
Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody paper :
......Here, we combined X-ray crystallography with computati …
- 1,299